Mercurial > repos > vijay > pancancer_targene_cell_line_predictions
changeset 0:872aab514d37 draft default tip
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
| author | vijay |
|---|---|
| date | Wed, 16 Dec 2020 23:30:22 +0000 |
| parents | |
| children | |
| files | macros.xml targene_cell_line_predictions.xml |
| diffstat | 2 files changed, 394 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Dec 16 23:30:22 2020 +0000 @@ -0,0 +1,229 @@ +<macros> + <token name="@VERSION@">0.1.9</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">papaa</requirement> + </requirements> + </xml> + + <xml name="stdio"> + <stdio> + <exit_code level="fatal" range="1:"/> + </stdio> + </xml> + + <xml name="inputs_basic"> + <param argument="--x_matrix" label="Filename of features to use in model" name="x_matrix" optional="true" type="data" format="tabular" help="data/pancan_rnaseq_freeze.tsv.gz"/> + <yield/> + <param argument="--filename_mut" label="Filename mutations" name="filename_mut" optional="true" type="data" format="tabular" help="data/pancan_mutation_freeze.tsv.gz"/> + <param argument="--filename_mut_burden" label="Filename of mutation burden" name="filename_mut_burden" optional="true" type="data" format="tabular" help="data/mutation_burden_freeze.tsv"/> + <param argument="--filename_sample" label="Filename of sample" name="filename_sample" optional="true" type="data" format="tabular" help="data/sample_freeze.tsv"/> + </xml> + + <token name="@INPUTS_BASIC@"><![CDATA[ + #if $x_matrix and $x_matrix is not None: + --x_matrix '$x_matrix' + #end if + #if $filename_mut and $filename_mut is not None: + --filename_mut '$filename_mut' + #end if + #if $filename_mut_burden and $filename_mut_burden is not None: + --filename_mut_burden '$filename_mut_burden' + #end if + #if $filename_sample and $filename_sample is not None: + --filename_sample '$filename_sample' + #end if + ]]> + </token> + + <xml name="inputs_genes_diseases"> + <param argument="--genes" label="Comma separated string of HUGO gene symbols" name="genes" optional="False" type="text" value="ERBB2,PIK3CA,KRAS,AKT1"/> + <param argument="--diseases" label="Comma sep string of TCGA disease acronyms. If no arguments are passed, filtering will default to options given in --filter_count and --filter_prop." name="diseases" optional="true" type="text" value="BLCA,BRCA,CESC,COAD,ESCA,LUAD,LUSC,OV,PRAD,READ,STAD,UCEC,UCS"/> + </xml> + + <token name="@INPUTS_GENES_DISEASES@"><![CDATA[ + #if $genes and $genes is not None: + --genes '$genes' + #end if + #if $diseases and str($diseases) != '': + --diseases '$diseases' + #end if + ]]> + </token> + + + <xml name="input_filename_raw_mut"> + <param argument="--filename_raw_mut" label="Filename of raw mut MAF" name="filename_raw_mut" optional="true" type="data" format="tabular" help="data/raw/mc3.v0.2.8.PUBLIC.maf"/> + </xml> + + <token name="@INPUT_FILENAME_RAW_MUT@"><![CDATA[ + #if $filename_raw_mut and $filename_raw_mut is not None: + --filename_raw_mut '$filename_raw_mut' + #end if + ]]> + </token> + + + <xml name="input_filename_burden"> + <param argument="--filename_burden" label="Burden file" name="filename_burden" optional="true" type="data" format="tabular" help="data/seg_based_scores.tsv"/> + </xml> + + <token name="@INPUT_FILENAME_BURDEN@"><![CDATA[ + #if $filename_burden and $filename_burden is not None: + --filename_burden '$filename_burden' + #end if + ]]> + </token> + + <xml name="input_filename_snaptron_samples"> + <param argument="--sample_file" label="SNAPTRON samples" name="sample_file" optional="true" type="data" format="tabular" help="scripts/snaptron/samples.tsv.gz"/> + </xml> + + <token name="@INPUT_FILENAME_SNAPTRON_SAMPLES@"><![CDATA[ + #if $sample_file and $sample_file is not None: + --sample_file '$sample_file' + #end if + ]]> + </token> + + + <xml name="input_filename_snaptron_junctions"> + <param argument="--junction_file" label="SNAPTRON junctions" name="junction_file" optional="true" type="data" format="tabular" help="scripts/snaptron/tp53_junctions.txt.gz"/> + </xml> + + <token name="@INPUT_FILENAME_SNAPTRON_JUNCTIONS@"><![CDATA[ + #if $junction_file and $junction_file is not None: + --junction_file '$junction_file' + #end if + ]]> + </token> + + <xml name="inputs_copy_number_file"> + <param argument="--filename_copy_loss" label="File with Copy number loss" name="filename_copy_loss" optional="true" type="data" format="tabular" help="data/copy_number_loss_status.tsv.gz"/> + <param argument="--filename_copy_gain" label="File with Copy number gain" name="filename_copy_gain" optional="true" type="data" format="tabular" help="data/copy_number_gain_status.tsv.gz"/> + </xml> + + <xml name="inputs_copy_number_class_file"> + <expand macro="inputs_copy_number_file" /> + <param argument="--filename_cancer_gene_classification" label="File with cancer gene classification table" name="filename_cancer_gene_classification" optional="true" type="data" format="tabular" help="data/cosmic_cancer_classification.tsv"/> + </xml> + + <xml name="inputs_copy_number_file_conditional"> + <conditional name="copy_number_conditional"> + <param argument="--copy_number" checked="false" label="Supplement Y matrix with copy number events" name="copy_number" type="boolean" truevalue="--copy_number" falsevalue=""/> + <when value="--copy_number"> + <expand macro="inputs_copy_number_file" /> + </when> + <when value=""/> + </conditional> + </xml> + + <xml name="inputs_copy_number_class_file_conditional"> + <conditional name="copy_number_conditional"> + <param argument="--copy_number" checked="false" label="Supplement Y matrix with copy number events" name="copy_number" type="boolean" truevalue="--copy_number" falsevalue=""/> + <when value="--copy_number"> + <expand macro="inputs_copy_number_class_file" /> + </when> + <when value=""/> + </conditional> + </xml> + + <token name="@INPUTS_COPY_NUMBER_FILE_PREFIX@"><![CDATA[ + #set $copy_number_conditional = type('',(object,),{'filename_copy_loss':$filename_copy_loss,'filename_copy_gain':$filename_copy_gain})() + ]]> + </token> + + <token name="@INPUTS_COPY_NUMBER_FILE@"><![CDATA[ + #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None: + --filename_copy_loss '$copy_number_conditional.filename_copy_loss' + #end if + #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None: + --filename_copy_gain '$copy_number_conditional.filename_copy_gain' + #end if + ]]> + </token> + + <token name="@INPUTS_COPY_NUMBER_FILE_CONDITIONAL@"><![CDATA[ + #if $copy_number_conditional.copy_number + $copy_number_conditional.copy_number + #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None: + --filename_copy_loss '$copy_number_conditional.filename_copy_loss' + #end if + #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None: + --filename_copy_gain '$copy_number_conditional.filename_copy_gain' + #end if + ##@INPUTS_COPY_NUMBER_FILE@ + #end if + ]]> + </token> + + <token name="@INPUTS_COPY_NUMBER_CLASS_FILE_PREFIX@"><![CDATA[ + #set $copy_number_conditional = type('',(object,),{'filename_copy_loss':$filename_copy_loss,'filename_copy_gain':$filename_copy_gain,'filename_cancer_gene_classification':$filename_cancer_gene_classification})() + ]]> + </token> + + <token name="@INPUTS_COPY_NUMBER_CLASS_FILE@"><![CDATA[ + #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None: + --filename_copy_loss '$copy_number_conditional.filename_copy_loss' + #end if + #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None: + --filename_copy_gain '$copy_number_conditional.filename_copy_gain' + #end if + #if $copy_number_conditional.filename_cancer_gene_classification and $copy_number_conditional.filename_cancer_gene_classification is not None: + --filename_cancer_gene_classification '$copy_number_conditional.filename_cancer_gene_classification' + #end if + ]]> + </token> + + <token name="@INPUTS_COPY_NUMBER_CLASS_FILE_CONDITIONAL@"><![CDATA[ + #if $copy_number_conditional.copy_number + $copy_number_conditional.copy_number + ## + #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None: + --filename_copy_loss '$copy_number_conditional.filename_copy_loss' + #end if + #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None: + --filename_copy_gain '$copy_number_conditional.filename_copy_gain' + #end if + #if $copy_number_conditional.filename_cancer_gene_classification and $copy_number_conditional.filename_cancer_gene_classification is not None: + --filename_cancer_gene_classification '$copy_number_conditional.filename_cancer_gene_classification' + #end if + ##@INPUTS_COPY_NUMBER_CLASS_FILE@ + #end if + ]]> + </token> + + <xml name="input_remove_hyper"> + <param argument="--remove_hyper" checked="false" label="Remove hypermutated samples" name="remove_hyper" type="boolean" truevalue="--remove_hyper" falsevalue=""/> + </xml> + <token name="@INPUT_REMOVE_HYPER@"><![CDATA[$remove_hyper]]></token> + + <xml name="input_alphas"> + <param argument="--alphas" label="the alphas for parameter sweep" name="alphas" optional="true" type="text" value="0.1,0.13,0.15,0.18,0.2,0.3,0.4,0.6,0.7"/> + </xml> + + <token name="@INPUTS_ALPHAS@"><![CDATA[ + #if $alphas and $alphas is not None: + --alphas '$alphas' + #end if + ]]> + </token> + + <xml name="input_l1_ratios"> + <param argument="--l1_ratios" label="the l1 ratios for parameter sweep" name="l1_ratios" optional="true" type="text" value="0.1,0.125,0.15,0.2,0.25,0.3,0.35"/> + </xml> + + <token name="@INPUTS_L1_RATIOS@"><![CDATA[ + #if $l1_ratios and $l1_ratios is not None: + --l1_ratios '$l1_ratios' + #end if + ]]> + </token> + <xml name="citations"> + <citations> + <yield /> + </citations> + </xml> +</macros> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/targene_cell_line_predictions.xml Wed Dec 16 23:30:22 2020 +0000 @@ -0,0 +1,165 @@ +<tool id="pancancer_targene_cell_line_predictions" name="PAPAA: PanCancer targene cell line predictions" version="@VERSION@"> + <description>targene status in ccle cell lines </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <version_command><![CDATA['papaa_targene_cell_line_predictions.py' --version]]></version_command> + <command><![CDATA[ + mkdir 'classifier' && + mkdir -p 'classifier/figures' && + mkdir -p 'classifier/figures/cell_line' && + mkdir -p 'classifier/tables' && + mkdir -p 'classifier/results' && + ln -s '${classifier_summary}' 'classifier/classifier_summary.txt' && + ln -s '${pancan_classifier_coefficients}' 'classifier/classifier_coefficients.tsv' && + ln -s '${nucleotide_mutation_scores}' 'classifier/tables/nucleotide_mutation_scores.tsv' && + ln -s '${amino_acid_mutation_scores}' 'classifier/tables/amino_acid_mutation_scores.tsv' && + papaa_targene_cell_line_predictions.py + --classifier_summary 'classifier' + #if $targenes and str($targenes): + --targenes '$targenes' + #end if + #if $path_genes and str($path_genes): + --path_genes '$path_genes' + #end if + #if $ccle_rnaseq and $ccle_rnaseq is not None: + --ccle_rnaseq '$ccle_rnaseq' + #end if + #if $ccle_mut and $ccle_mut is not None: + --ccle_mut '$ccle_mut' + #end if + #if $ccle_maf and $ccle_maf is not None: + --ccle_maf '$ccle_maf' + #end if + #if $gdsc_rnaseq and $gdsc_rnaseq is not None: + --gdsc_rnaseq '$gdsc_rnaseq' + #end if + #if $gdsc_mut and $gdsc_mut is not None: + --gdsc_mut '$gdsc_mut' + #end if + #if $gdsc1_phar and $gdsc1_phar is not None: + --gdsc1_phar '$gdsc1_phar' + #end if + #if $gdsc2_phar and $gdsc2_phar is not None: + --gdsc2_phar '$gdsc2_phar' + #end if + > '${log}' + ]]> + </command> + <inputs> + <param argument="--classifier_summary" label="Classifier data" name="classifier_summary" optional="false" type="data" format="txt" help="classifer_summary.txt"/> + <param label="pancancer classifier coefficients" name="pancan_classifier_coefficients" optional="false" type="data" format="tabular" help="classifier_coefficients.tsv"/> + <param label="nucleotide mutation scores" name="nucleotide_mutation_scores" optional="false" type="data" format="tabular" help="nucleotide_mutation_scores.tsv"/> + <param label="amino acid mutation scores" name="amino_acid_mutation_scores" optional="false" type="data" format="tabular" help="amino_acid_mutation_scores.tsv"/> + <param argument="--targenes" label="Comma separated string of HUGO targene symbols" name="targenes" optional="False" type="text" value="ERBB2_MUT,PIK3CA_MUT,KRAS_MUT,AKT1_MUT"/> + <param argument="--path_genes" label="string of the genes to extract or genelist file" name="path_genes" optional="true" type= "data" format="txt"/> + <param argument="--ccle_rnaseq" label="Filename ccle rnaseq data" name="ccle_rnaseq" optional="false" type="data" format="tabular" help="data/ccle_rnaseq_genes_rpkm_20180929_mod.tsv"/> + <param argument="--ccle_mut" label="Filename ccle mutational data" name="ccle_mut" optional="true" type="data" format="txt" help="data/CCLE_MUT_CNA_AMP_DEL_binary_Revealer.gct"/> + <param argument="--ccle_maf" label="Filename ccle variant data" name="ccle_maf" optional="true" type="data" format="txt" help="data/CCLE_DepMap_18Q1_maf_20180207.txt" /> + <param argument="--gdsc_rnaseq" label="Filename gdsc rnaseq data" name="gdsc_rnaseq" optional="false" type="data" format="tabular" help="data/GDSC_EXP_CCLE_converted_name.tsv"/> + <param argument="--gdsc_mut" label="Filename gdsc mutational data" name="gdsc_mut" optional="true" type="data" format="tabular" help="data/GDSC_CCLE_common_mut_cnv_binary.tsv"/> + <param argument="--gdsc1_phar" label="Filename for gdsc1 pharmacological data file" name="gdsc1_phar" optional="false" type="data" format="txt" help="data/gdsc1_ccle_pharm_fitted_dose_data.txt"/> + <param argument="--gdsc2_phar" label="Filename for gdsc2 pharmacological data file" name="gdsc2_phar" optional="false" type="data" format="txt" help="data/gdsc2_ccle_pharm_fitted_dose_data.txt"/> + </inputs> + <outputs> + <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/> + <data format="png" name="ccle_histogram" label="${tool.name} on ${on_string} (ccle_histogram.png)" from_work_dir="classifier/figures/ccle_histogram.png"/> + <data format="tabular" name="ccle_targene_classifier_scores" label="${tool.name} on ${on_string} (ccle_targene_classifier_scores.tsv)" from_work_dir="classifier/tables/ccle_targene_classifier_scores.tsv"/> + <data format="pdf" name="ccle_targene_WT_MUT_predictions" label="${tool.name} on ${on_string} (ccle_targene_WT_MUT_predictions.pdf)" from_work_dir="classifier/figures/cell_line/ccle_targene_WT_MUT_predictions.pdf"/> + <data format="csv" name="updated_data_nucleotide_scores" label="${tool.name} on ${on_string} (updated_data_nucleotide_scores.csv)" from_work_dir="classifier/tables/updated_data_nucleotide_scores.csv"/> + <data format="csv" name="updated_data_aminoacid_scores" label="${tool.name} on ${on_string} (updated_data_aminoacid_scores.csv)" from_work_dir="classifier/tables/updated_data_aminoacid_scores.csv"/> + <data format="png" name="gdsc_scores_histogram" label="${tool.name} on ${on_string} (gdsc_scores_histogram.png)" from_work_dir="classifier/figures/gdsc_scores_histogram.png"/> + <data format="tabular" name="gdsc_targene_classifier_scores" label="${tool.name} on ${on_string} (gdsc_targene_classifier_scores.tsv)" from_work_dir="classifier/tables/gdsc_targene_classifier_scores.tsv"/> + <data format="pdf" name="gdsc_targene_WT_MUT_predictions" label="${tool.name} on ${on_string} (gdsc_targene_WT_MUT_predictions.pdf)" from_work_dir="classifier/figures/cell_line/gdsc_targene_WT_MUT_predictions.pdf"/> + <data format="tabular" name="gdsc1_targene_pharmacology_predictions" label="${tool.name} on ${on_string} (gdsc1_targene_pharmacology_predictions.tsv)" from_work_dir="classifier/tables/gdsc1_targene_pharmacology_predictions.tsv"/> + <data format="tabular" name="gdsc2_targene_pharmacology_predictions" label="${tool.name} on ${on_string} (gdsc2_targene_pharmacology_predictions.tsv)" from_work_dir="classifier/tables/gdsc2_targene_pharmacology_predictions.tsv"/> + <data format="tabular" name="gdsc1_ccle_targene_pharmacology_predictions" label="${tool.name} on ${on_string} (gdsc1_ccle_targene_pharmacology_predictions.tsv)" from_work_dir="classifier/tables/gdsc1_ccle_targene_pharmacology_predictions.tsv"/> + <data format="tabular" name="gdsc2_ccle_targene_pharmacology_predictions" label="${tool.name} on ${on_string} (gdsc2_ccle_targene_pharmacology_predictions.tsv)" from_work_dir="classifier/tables/gdsc2_ccle_targene_pharmacology_predictions.tsv"/> + </outputs> + <tests> + <test> + <param name="classifier_summary" value="classifier_summary.txt" ftype="txt"/> + <param name="pancan_classifier_coefficients" value="classifier_coefficients.tsv" ftype="tabular"/> + <param name="nucleotide_mutation_scores" value="nucleotide_mutation_scores.tsv" ftype="tabular"/> + <param name="amino_acid_mutation_scores" value="amino_acid_mutation_scores.tsv" ftype="tabular"/> + <param name="targenes" value="ERBB2_MUT,PIK3CA_MUT,KRAS_MUT,AKT1_MUT"/> + <param name="path_genes" value="path_genes.txt" ftype="txt"/> + <param name="ccle_rnaseq" value="ccle_rnaseq_genes_rpkm_20180929_mod_t5p.tsv.gz" ftype="tabular"/> + <param name="ccle_mut" value="CCLE_MUT_CNA_AMP_DEL_binary_Revealer.gct.gz" ftype="tabular"/> + <param name="ccle_maf" value="CCLE_DepMap_18Q1_maf_20180207_t1p.txt.gz" ftype="txt"/> + <param name="gdsc_rnaseq" value="GDSC_EXP_CCLE_converted_name_t10p.tsv.gz" ftype="tabular"/> + <param name="gdsc_mut" value="GDSC_CCLE_common_mut_cnv_binary.tsv.gz" ftype="tabular"/> + <param name="gdsc1_phar" value="gdsc1_ccle_pharm_fitted_dose_data_t10p.txt.gz" ftype="txt"/> + <param name="gdsc2_phar" value="gdsc2_ccle_pharm_fitted_dose_data_t10p.txt.gz" ftype="txt"/> + <output name="log" file="targene_cell_line_predictions_Log.txt" lines_diff="2"/> + <output name="ccle_histogram" file="ccle_histogram.png" compare="sim_size" delta="50"/> + <output name="ccle_targene_classifier_scores" file="ccle_targene_classifier_scores.tsv" /> + <output name="ccle_targene_WT_MUT_predictions" file="ccle_targene_WT_MUT_predictions.pdf" compare="sim_size" delta="100"/> + <output name="updated_data_nucleotide_scores" file="updated_data_nucleotide_scores.csv" /> + <output name="updated_data_aminoacid_scores" file="updated_data_aminoacid_scores.csv" /> + <output name="gdsc_scores_histogram" file="gdsc_scores_histogram.png" /> + <output name="gdsc_targene_classifier_scores" file="gdsc_targene_classifier_scores.tsv" /> + <output name="gdsc_targene_WT_MUT_predictions" file="gdsc_targene_WT_MUT_predictions.pdf" compare="sim_size" delta="50"/> + <output name="gdsc1_targene_pharmacology_predictions"> + <assert_contents> + <has_line line="	GDSC1_cell_line	NLME_CURVE_ID	COSMIC_ID	SANGER_MODEL_ID	TCGA_DESC	DRUG_ID	Compound	PUTATIVE_TARGET	PATHWAY_NAME	MIN_CONC	MAX_CONC	LN_IC50	AUC	RMSE	Z_SCORE	tissue	ERBB2_MUT	PIK3CA_MUT	KRAS_MUT	AKT1_MUT	targene_status	weight	sample_name	predictions" /> + <has_n_columns n="25" /> + <has_n_lines n="10281" /> + </assert_contents> + </output> + <output name="gdsc2_targene_pharmacology_predictions"> + <assert_contents> + <has_line line="	GDSC1_cell_line	NLME_CURVE_ID	COSMIC_ID	SANGER_MODEL_ID	TCGA_DESC	DRUG_ID	Compound	PUTATIVE_TARGET	PATHWAY_NAME	MIN_CONC	MAX_CONC	LN_IC50	AUC	RMSE	Z_SCORE	tissue	ERBB2_MUT	PIK3CA_MUT	KRAS_MUT	AKT1_MUT	targene_status	weight	sample_name	predictions" /> + <has_n_columns n="25" /> + <has_n_lines n="10281" /> + </assert_contents> + </output> + <output name="gdsc1_ccle_targene_pharmacology_predictions" file="gdsc1_ccle_targene_pharmacology_predictions.tsv" /> + <output name="gdsc2_ccle_targene_pharmacology_predictions" file="gdsc2_ccle_targene_pharmacology_predictions.tsv" /> + </test> + </tests> + <help><![CDATA[ + + **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/viz/papaa_targene_cell_line_predictions_mod.py:** + + **Inputs:** + --targenes comma separated string of HUGO symbols for target genes or targenes_list.csv file + --path_genes comma separated string of HUGO symbols for all genes in the target pathway or path_genes.txt file + --classifier_summary String of the location of classifier_summary file + --ccle_rnaseq Filename of CCLE gene expression data file + --ccle_mut Filename of CCLE cell lines/gene mutations data file + --ccle_maf Filename of CCLE mutational variant level data file + --gdsc_rnaseq Filename of GDSC gene expression data file + --gdsc_mut Filename of GDSC cell lines/gene mutations data file + --gdsc1_phar Filename of GDSC1 pharmacological response data + --gdsc2_phar Filename of GDSC2 pharmacological response data + + **Outputs:** + Generate predictions for CCLE data using targene classifier(ccle_histogram.png) + + Generate classifier scores for CCLE cell lines and combines CCLE mutational data and variant data with classifier scores (ccle_targene_classifier_scores.tsv) + + Performs t-test on classifier weights across targene mutant vs targene wildtype cell-line groups(ccle_targene_WT_MUT_predictions.pdf) + + Add CCLE nucleotide scores at variant level and update nucleotide_mutation_scores.tsv (updated_data_nucleotide_scores.csv) + + Add CCLE protein scores at variant level and update aminoacid_mutation_scores.tsv (updated_data_aminoacid_scores.csv) + + Generate predictions for GDSC data using targene classifier(gdsc_scores_histogram.png) + + Generate classifier scores for GDSC cell lines and combines CCLE mutational data and variant data with classifier scores (gdsc_targene_classifier_scores.tsv) + + Performs t-test on classifier weights across targene mutant vs targene wildtype cell-line groups(gdsc_targene_WT_MUT_predictions.pdf) + + Apply GDSC classifier scores to evaluate GDSC1 pharmacological data response(gdsc1_targene_pharmacology_predictions.tsv) + + Apply GDSC classifier scores to evaluate GDSC2 pharmacological data response(gdsc2_targene_pharmacology_predictions.tsv) + + Apply CCLE classifier scores to evaluate GDSC1 pharmacological data response(gdsc1_ccle_targene_pharmacology_predictions.tsv) + + Apply CCLE classifier scores to evaluate GDSC2 pharmacological data response(gdsc2_ccle_targene_pharmacology_predictions.tsv) ]]> + </help> + <expand macro="citations" /> +</tool>